Rhythm Thief: Second Season
by The Mormon And Otaku
Summary: Six months. Six months ago the infamous Phantom R disappeared without a trace, leaving the people of France in a state of peace. However, within those six months, someone has been plotting. Now with his plans complete, Raphael must band with his old friends and partners to stop Neapolitan's plans. least, that's what he thought. But not every story has a happy ending.
1. Chapter 1

===(Isaac)===

Standing on top of the Eiffel Tower was truly a sight to behold. The wind blowing on your face, the sight of Paris bustling with people….

I would be enjoying it if **Neapolitan** wasn't standing here with me.

He stood there with a smug look on his face as if everyone was already kneeling to him, which probably wasn't too far from the truth. It was tempting to just push him off and let him die, but there was one reason that I couldn't. The reason why I was doing all of this in the first place.

"Raphael," Neapolitan muttered. "He is a formidable foe. I honestly didn't think he would best Leonard or my forces." He pauses as he slowly turns his head towards me. "Dare I say, he might be a threat?"

I narrow my eyes. His tone may have sounded light, but I could tell that it was full of malice and anger. Still, I reply in a calm voice, "No, he won't. Even with his skills he will barely be a flea in your plan."

"Hmmm…." Neapolitan was toying with me. He had complete confidence in his plan, but he loved to test my emotions. Unfortunately, I could only play the role of the monkey while he played as the ringmaster. "Why yes, I suppose you are right." He walks past me towards the stairs, beckoning me with his arm. "Come, Isaac. There is much to be done."

"Of course my lord." I follow him, my heart full of dread for what was about to happen. _Raphael. If you received my warning, then please understand. This is all for you._

===(Charlotte)===

"Charlie! For the millionth time, pay attention!"

"Ack! I'm sorry, I'm sorry!"

The teacher sighs and gets back to the lesson. I tried to pay attention, I really did, but it was just…. So…. _Boring!_ I know that it was unbecoming of me to not pay attention in school when I wanted to be a detective, but I couldn't help it if I was terrible at math. _Besides, I have more important things to worry about…._

Salvation finally came when the school bell rang for the last time today. I quickly grab my backpack and run out the door before the teacher could give me another lecture. My house was only a three minute walk from school, making my trip home a fast one. Usually I got my homework done as soon as I got home so that I could enjoy the rest of my day. Today, however, I had different plans in mind. I threw my backpack onto my bed and changed into my work clothes, which I found to be more comfortable than my dresses. Along with my clothes I grab a satchel and put in a pair of handcuffs, my phone, a notebook with three pencils and a pencil sharpener, and most importantly, the clue that I found at the hideout underneath the louvre yesterday.

I decided not to study it just yet in case anybody came over and interrupted me. So instead, I go to the park. It was a nice place that made me feel at ease, and allowed me to have space to study the clue in peace.

Looking around to see if anybody was watching me, I carefully pull out the mysterious item that I had found: A letter. When I found it, I immediately read it, though it didn't make any sense to me. Unfortunately I had soccer practice that day and couldn't investigate it more. Right now, though, I could take as much time as I wanted to.

Settling down on a bench, I hunch over and re-read it's contents: ' _I know that you're confused about all this, but you need to forget about all this. It's already too dangerous for you to be involved with all this, but if you keep meddling with this, then you'll face grave consequences. There are horrors that are beyond your imagination, so please: Stay away._

 _Forget about me._

 _Pretend that I didn't exist. Live your life. All that will happen in trying to help me will just result in pain and misery. Please, Raphael….'_

It ended abruptly there. When I first saw this I was confused, but after I looked at it some more, I found that it looked like it had been torn apart. There was more to this letter, which frustrated me since I couldn't piece the rest of it. _From the looks of it it sounds like one of those goons had a child. Maybe that child can lead me to answers about what happened six months ago._ The events swirl inside my head, replaying over and over again like a movie. It all seemed like a movie too. None of it made any sense. _When queen Elizabeth recovered, she said to forget about it all. My father may have turned a blind eye to it all, but I won't. I refuse to!_

Putting the letter back in my satchel, I make my way to the police station. _I know of a few people who can analyze a person's handwriting. With this, I'll be able to identify at least someone who's connecting with that incident! But this Raphael person was also involved with them in some way. The only people I know that were part of that incident was my father, me, queen Elizabeth and her daughter, and-_

I stop dead in my tracks as a possibility popped into my mind. _Phantom R…. Could he be this Raphael person?_ There wasn't any evidence to point to this, but if this letter really was addressed to him, then this would be a major lead to uncovering Phantom R. I change my walk into a run, eager to share this with father.

===(Raphael)===

"Achoo!"

I pull out my handkerchief and wipe my nose. "Man, it's cold out here, eh Fondue?" He barks in reply. After spending so much time with him I've come to understand his barks. Sorta.

Right now I was taking him out for a walk in the streets of Paris. _I missed being able to walk around without the cops chasing me every few minutes. Then again, I do miss the thrill of playing tag with them._ It felt like years ago, though in reality it hadn't been that long ago.

My retirement.

It was a few days after I uncovered defeated Leonard that I went searching for another lead for my father. On a whim I checked the place where I first saw a glimpse of dad, hoping to find another lead. What I found was a letter with my dad's handwriting, and for a minute I thought that I had the key to finally get dad back.

But boy was I wrong.

' _...Though I can't explain what I mean, know that I have to do what I'm doing, even if it pains me not being able to be a better father to you.I know that it doesn't justify my actions in the slightest, and I accept full consequences for my actions._

 _Raphael, you may want to help me still, but know that I am beyond hope. However, you're free to live your life in any way you want to. You have the power to control your own destiny, unlike me. Value what you have, because at any moment, it can vanish from your life. Take it from me, I would know._

 _I love you my son, now and forever. You will always be in my heart._

 _Goodbye Raphael. Or, as you might prefer, Phantom R.'_

Reading that letter nearly made me pass out. I was so shocked that I didn't even realize that the letter was missing it's top half. When I did realize this, it was too late. If I tried to go back to the hideouts, the mastermind behind all this would probably wonder why I would go back, which might put dad in danger if he ever caught wind of the warning letter he gave me. So instead, I was going to wait until this 'big plan' finally came into light. It was like having a small vacation, but…. Not.

"*Ruff!*"

Fondue's barking snaps me out of my thoughts. Looking up, I saw that he was chasing a squirrel. "Ugh, not again…." I start to go after him.

"Hello?"

A familiar voice startles me, and when I turn around, I almost say her name out loud. Standing there was Charlotte, or as she would rather prefer, Charlie.

It seemed that she saw Fondue running around, which meant that she would be on lookout for Phantom R. _If she starts looking at me, she might find out my alter ego. I need to get out of here._ With quick thinking, I make a plan.

"Huh?" I pull out my phone and pretend to be getting a call. "Grandma? Hey, what's up! ….Oh. Oh okay, I'll head back now." Still pretending, I tuck the phone back into my pocket and break into a jog. Charlotte called after me, but I ignore her. After jogging a few blocks, I look behind me and see that Charlotte wasn't there. _Thank goodness. It would've been a hassle to deal with the police investigating my place._ The question now is how I would find Fondue….

"HEY!" I try to catch up to the boy, but I trip and fall on my face. _Agh, that hurts….._ When I look up, the boy was gone. I curse to myself as I get up. _I wonder who that boy was. He seemed familiar too. But more importantly…._

I look at what he dropped. "A piece of paper?"


	2. Chapter 2: A void reunion

**N** **ote: It's been a while since I've made this fanfiction, but** **I do plan to finish this story. Rhythm Thief is one of my favorite games, and it deserves a lot of love. I know that fanfiction for series like this tend to go unfinished, which is the LAST thing that I want. Apologies for those who're anticipating the next chapters. I hope you'll all stick around until the very end!**

===(Raphael)===

 _I screwed up big time._

When I reunited with Fondue, I realized that the letter I had was gone. I pieced together that Charlotte most likely had it, and that she was probably trying to give it to me when I dropped it. It was beyond embarrassing. Me, Phantom R by night, the boy that heisted dozens of invaluable pieces of art and safely returned them without ever being caught accidentally dropped a piece of paper from his pocket. I would never hear the end of it from Charlotte.

 _Speaking of which…._ The police would no doubt come for me, but I couldn't let them cage up Fondue. Even though I was a child living by himself, there was a place that Fondue would be safe at: Marie's mansion. She loved Fondue, and was also the only other friend that Fondue had.

 _Marie…._

My walking pace slows as I think back to her. She was actually my first friend. Ever since I became the Rhythm Thief, I haven't been able to live a normal life. I was moved to an orphanage for my own benefit, but I hated it there. The other kids bullied me so that they would feel better about not having parents, and I never got along with the caretakers. It was a bleak part of my life that I didn't like to look back on.

But that was all in the past now. I moved on from those dark times and came out with the strength that I needed to become Phantom R. Besides, the skills that I've developed as a kid helped me out on infiltrations, so it wasn't all that bad.

Of course, I dearly missed Marie these past six months, and I knew I would have to inevitably call for duchess Elizabeth's and Marie's help again. However, I decided to cut ties with them when I went into my temporary retirement. I knew the pain of wanting to reunite with your parent again, and I didn't want to ruin that with my problems .Still, I knew that she must've missed me as much as I missed her, so I made a letter to Marie before I left my apartment, which I squeezed in between Fondue's collar and fur. It wasn't much, but it would suffice for now.

When we get near her establishment, I stop walking. Most of the maids and butlers that worked there knew my face, and would most likely call for Marie or Elizabeth if they saw me. If that happened, then they would get involved with the police, and things would just get even more complicated. I knew that my decision wasn't much better, but it would keep Marie from getting heat from the cops.

I get down on my knees and tell my friend, "Alright Fondue, I need you to deliver this letter to Marie for me, okay?"

He barked questioningly at me, asking me what I was going to do.

"Don't worry, I'll catch up with you later." His eyes still seemed uncertain, but his let out a bark of trust. "Thank you Fondue." I then pull him into a hug, which he responds to with a lick. In that moment, I found it hard to let go of him. I didn't know when I'd be back for him. It could be days, weeks, even months. Still, I was determined to see my decision through. With tears in my eyes, I whisper to him, "Fondue…. You'll always be my partner in crime."

"*Wuff!*"

When I let him go he instantly takes off running towards the gate, probably excited to see Marie again after so long. Silently I whispered into the air, "Please take care of him Marie."

I then walk back to my soon-not-to-be home and lay down on my bed. It would be a while before I get to lay on my mattress again.

===(Marie)===

I stretch my arms as I set my violin down, my bones cracking in response. Even though I loved playing music to my heart's content, I was keen on frequent breaks.

Usually when I practiced on my violin it would be in front of others, whether it be with mom or a staff member. This time however, I was playing it in a secluded area in the garden. I enjoyed playing outside as well as I did indoors, but this time I felt like I was playing for a different reason. It felt like someone was asking me for help, to give them strength. _Could it be Raphael?_ That was my first thought, and while I hoped that it really was him, I couldn't help but feel a bad premonition. Where Raphael was, there was usually trouble.

Suddenly, a loud bark shattered my thoughts. It was a familiar bark, one that I knew fairly well. I turn around, and my suspicions were confirmed when I saw Fondue running towards me at full speed. I cried out loudly, "FONDUE!" I kneel down and hold out my arms to welcome the dog. Without hesitation he jumps into a hug, showering me with licks as he excitedly wagged his tail. "Oooohhh, I missed you so much Fondue!" As I keep petting him, I realized that Raphael wasn't there. _Is he about to pop up behind me?_

I turn around and look to see if he was already next to me, but as I looked he was nowhere to be found. Unconsciously I ask the dog, "Hey Fondue, where's Raphael?"

As I said this I thought to myself that it was a silly idea to ask him since he's, well, a dog. To my surprise, he lays down and barks at me. For a second I thought that he wanted me to pet him some more, but when I went to do so I noticed something in his collar. It was an envelope.

It immediately registered in my mind that it was from Raphael. Ecstatic, I quickly open the letter and read it:

' _Hello Marie. I'm sorry that I couldn't say that to you in person, along with not keeping in touch with you for the past six months. The reason why I held off on a reunion was because I wanted you to be able to make up some of your lost time with your mother, Elizabeth. You've been waiting for her all your life, and you deserved to have some 'mother and daughter' time with her. I hope you've made some good memories with her._

 _As for my lack of presence right now, well…. I made a mistake._

 _I found a clue that could lead me to my father, but it also had my identity as Phantom R on it as well. Charlotte has it, and she will most definitely arrest me. I'm not going to run from this though. In fact, this may be a golden opportunity to find out who the mastermind behind Leonard and his lackeys is. I don't have time to write why or how, but I'll explain it to you soon._

 _Marie, I know it's unfair of me to ask after leaving you in the dark all this time, but I need a favor from you. Please take care of Fondue. He's the only family I have right now. And please, don't get involved with me getting arrested. Nobody at the police station knows that you and I are acquainted, and I want to keep it that way. I'll manage to find a way out of this mess, and as soon as I get out I'll come back for you. I promise this time._

 _You should enjoy today with your mother. It might be the last normal day you'll have for a while._

 _Sincerely,_

 _Raphael_

I was in shock when I finished reading the letter, so much so that I didn't notice one of the maids calling out to me until she tapped my shoulder. "Lady Marie, is everything alright?"

I quickly stuff the letter into my pocket and shoot straight up onto my feet. "I-I'm fine! I was just, uh, writing a list of books that I wanted to check out from the library!"

I was a terrible liar.

Thankfully, she seemed to be very trusting. "Oh? In that case, I'm sorry for intruding." She politely bows her head to me, which made me feel a bit guilty for lying to her. "By the way, when did this dog get here?"

"Dog? ….The dog!" I forgot all about Fondue, and I stumble for words as I try to come up with an explanation. "He's…. Well…. A-a friend of mine asked me to take care of him!" It was the truth, though I left out the part about Fondue being Phantom R's dog.

I was fortunate again. The maid was a bit new here, so she didn't know that Fondue was Raphael's companion, unlike the other maids and butlers who worked here since Raphael sneaked into the mansion. "Well, it isn't my place to ridicule you, but please inform your mother about this."

I let out a sigh of relief. "I will. Thank you."

She smiles at me and says, "I'm just doing my duty," before she goes back to her task. When she was out of sight, I take a look at Fondue. He was wagging his tail, and his face was lit up with cheer.

I was dreading the moment he realized that Raphael wouldn't be coming back for a while.


End file.
